I'd say Species 8472 that even Borgs feared but I agree with Quark's, the deadliest ennemies of Voyager (and all others series of ST's franchise), were writers (and producers), undoubtedly!
I had a secret liking for Species 8472 but felt sympathy for them. They usually were acting in defense or retaliation because the Borg and the Federation attacked them first. I don't get how the Caretaker had such power even in his dying days and yet his mate was so easily overcome. At the end of the day Humans and their capabilities constitute the potential to be the Deadliest Enemy. Henry Starling from Futures End I submit as exhibit one..
Definitely Species 8472 (the Borg were losing to them!), although they were short lived in the series. Next to them, definitely the Borg... although I still feel the whole "queen" bit destroyed an important menacing aspect to the Borg. That "faceless collective" was ominous. Just watch that first encounter in TNG... it reminds you of how horrifying these creatures were, before being more "humanized" with a queen leader. One thing that really pissed me off about Enterprise was the introduction of the Borg. Total canon violation. No need for it. But I guess with the dire ratings problem, they couldn't resist leveraging them. Origin totally belongs to TNG and that should never have been "rewritten."
The look of Species 8472 was everything a human thinks of as scary alien too. They were pretty intelligent too and able to adapt. It would have been justice if they had been the ones to degrade the Borg in Endgame.